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chore: update base image, vcf2maf, VEP, Cromwell, lockfile deps #84

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Jun 3, 2024
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chore: update base image, vcf2maf, VEP, Cromwell, lockfile deps #84

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2 changes: 1 addition & 1 deletion .github/workflows/test.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,7 @@ jobs:
with:
python-version: ${{ matrix.python-version }}
- name: Install Poetry
run: python -m pip install poetry==1.8.2
run: python -m pip install poetry
- name: Install dependencies
run: python -m poetry install
- name: Test
Expand Down
14 changes: 6 additions & 8 deletions Dockerfile
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Expand Up @@ -3,11 +3,10 @@ FROM --platform=$BUILDPLATFORM debian:bullseye-slim AS downloaded-deps
SHELL ["/bin/bash", "-c"]

# Install VCF2MAF
# - support VEP v107+ by patching vcf2maf to remove references to removed --af_esp option
# TODO: I don't like /opt as a home for these

WORKDIR /tmp/vcf2maf
ENV VCF2MAF_VERSION=1.6.21
ENV VCF2MAF_VERSION=1.6.22
RUN apt-get update -y && \
apt-get install -y curl git unzip wget && \
echo "https://github.com/mskcc/vcf2maf/archive/refs/tags/v${VCF2MAF_VERSION}.zip" && \
Expand All @@ -16,12 +15,11 @@ RUN apt-get update -y && \
mv "vcf2maf-${VCF2MAF_VERSION}" vcf2maf && \
mkdir -p /opt/data && \
cp vcf2maf/*.pl /opt && \
sed -i '/ --af_esp/d' /opt/vcf2maf.pl && \
cp -r vcf2maf/data /opt/data && \
rm -rf vcf2maf

# Download Cromwell + WOMtool
ENV CROMWELL_VERSION=86
ENV CROMWELL_VERSION=87
WORKDIR /
RUN curl -L \
https://github.com/broadinstitute/cromwell/releases/download/${CROMWELL_VERSION}/cromwell-${CROMWELL_VERSION}.jar \
Expand All @@ -32,7 +30,7 @@ RUN curl -L \


# Clone (but don't install yet) Ensembl-VEP
ENV VEP_ENSEMBL_GIT_VERSION=111.0
ENV VEP_ENSEMBL_GIT_VERSION=112.0
RUN git clone --depth 1 -b "release/${VEP_ENSEMBL_GIT_VERSION}" https://github.com/Ensembl/ensembl-vep.git && \
chmod u+x ensembl-vep/*.pl

Expand All @@ -49,7 +47,7 @@ RUN curl -L https://github.com/Ensembl/ensembl-xs/archive/2.3.2.zip -o ensembl-x

WORKDIR /

FROM ghcr.io/bento-platform/bento_base_image:python-debian-2024.04.01 AS base-deps
FROM ghcr.io/bento-platform/bento_base_image:python-debian-2024.06.01 AS base-deps

SHELL ["/bin/bash", "-c"]

Expand Down Expand Up @@ -129,8 +127,8 @@ COPY --from=downloaded-deps /cromwell.jar /cromwell.jar
COPY --from=downloaded-deps /womtool.jar /womtool.jar

# - Copy Ensembl-VEP
COPY --from=ensemblorg/ensembl-vep:release_111.0 /usr/share/perl/5.34.0/CPAN /opt/vep
COPY --from=ensemblorg/ensembl-vep:release_111.0 /opt/vep /opt/vep
COPY --from=ensemblorg/ensembl-vep:release_112.0 /usr/share/perl/5.34.0/CPAN /opt/vep
COPY --from=ensemblorg/ensembl-vep:release_112.0 /opt/vep /opt/vep

ENTRYPOINT [ "bash", "./entrypoint.bash" ]
CMD [ "bash", "./run.bash" ]
14 changes: 6 additions & 8 deletions dev.Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -3,11 +3,10 @@ FROM --platform=$BUILDPLATFORM debian:bullseye-slim AS downloaded-deps
SHELL ["/bin/bash", "-c"]

# Install VCF2MAF
# - support VEP v107+ by patching vcf2maf to remove references to removed --af_esp option
# TODO: I don't like /opt as a home for these

WORKDIR /tmp/vcf2maf
ENV VCF2MAF_VERSION=1.6.21
ENV VCF2MAF_VERSION=1.6.22
RUN apt-get update -y && \
apt-get install -y curl git unzip wget && \
echo "https://github.com/mskcc/vcf2maf/archive/refs/tags/v${VCF2MAF_VERSION}.zip" && \
Expand All @@ -16,12 +15,11 @@ RUN apt-get update -y && \
mv "vcf2maf-${VCF2MAF_VERSION}" vcf2maf && \
mkdir -p /opt/data && \
cp vcf2maf/*.pl /opt && \
sed -i '/ --af_esp/d' /opt/vcf2maf.pl && \
cp -r vcf2maf/data /opt/data && \
rm -rf vcf2maf

# Download Cromwell + WOMtool
ENV CROMWELL_VERSION=86
ENV CROMWELL_VERSION=87
WORKDIR /
RUN curl -L \
https://github.com/broadinstitute/cromwell/releases/download/${CROMWELL_VERSION}/cromwell-${CROMWELL_VERSION}.jar \
Expand All @@ -32,7 +30,7 @@ RUN curl -L \


# Clone (but don't install yet) Ensembl-VEP
ENV VEP_ENSEMBL_GIT_VERSION=111.0
ENV VEP_ENSEMBL_GIT_VERSION=112.0
RUN git clone --depth 1 -b "release/${VEP_ENSEMBL_GIT_VERSION}" https://github.com/Ensembl/ensembl-vep.git && \
chmod u+x ensembl-vep/*.pl

Expand All @@ -49,7 +47,7 @@ RUN curl -L https://github.com/Ensembl/ensembl-xs/archive/2.3.2.zip -o ensembl-x

WORKDIR /

FROM ghcr.io/bento-platform/bento_base_image:python-debian-2024.04.01 AS base-deps
FROM ghcr.io/bento-platform/bento_base_image:python-debian-2024.06.01 AS base-deps

LABEL org.opencontainers.image.description="Local development image for Bento WES."
LABEL devcontainer.metadata='[{ \
Expand Down Expand Up @@ -136,8 +134,8 @@ COPY --from=downloaded-deps /cromwell.jar /cromwell.jar
COPY --from=downloaded-deps /womtool.jar /womtool.jar

# - Copy Ensembl-VEP
COPY --from=ensemblorg/ensembl-vep:release_111.0 /usr/share/perl/5.34.0/CPAN /opt/vep
COPY --from=ensemblorg/ensembl-vep:release_111.0 /opt/vep /opt/vep
COPY --from=ensemblorg/ensembl-vep:release_112.0 /usr/share/perl/5.34.0/CPAN /opt/vep
COPY --from=ensemblorg/ensembl-vep:release_112.0 /opt/vep /opt/vep

ENTRYPOINT [ "bash", "./entrypoint.bash" ]
CMD [ "bash", "./run.dev.bash" ]
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